Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

Abstract

Aromatic π-π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA-polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene-PDI interactions that were found to directly influence duplex stability. As the pyrene-PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene-PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π-π stacking interactions.

Keywords: DNA; hybridization; nucleic acids; perylenediimide; pyrene.

Figure 1

(A) Structures of 1,8-dialkynylpyrene (Y) and PDI (E); (B) illustration of the electrostatic potential surface of 1,8-diprop-1-ynylpyrene (left) and N,N’-dimethyl-PDI (right); (C) illustration of duplex formation with chimeric oligomers; (D) hybrids 1*2 to 1*6. The number of pyrene–PDI interactions increases from left to right.

Figure 2

A plot of melting temperature (T_m) versus the number of pyrene–PDI interactions for duplexes 1*2 to 1*6 (from left to right) presented in Table 1. The T_m was recorded at 260 nm; R² = 0.987. The red triangle represents the T_m of the control hybrid 7*6.

Figure 3

UV–vis absorption spectra (scaled) of duplexes 1*2 (blue) and 1*6 (red) at 20 °C. Conditions: see Table 1.

Figure 4

UV–vis absorption spectra (scaled) of duplexes 1*2 to 1*6 at 20 °C. Conditions: see Table 1.

Figure 5

Temperature-dependent UV–vis absorption spectrum of 1*2. Conditions: see Table 1.

Figure 6

Fluorescence spectra of oligomer 1 (black), duplex 1*2 (blue) and duplex 1*6 (red) at 20 °C. Excitation: 370 nm. Conditions: see Table 1.

Figure 7

PAGE experiment. All oligomers were used in a total amount of 150 pmol in 10 mM sodium phosphate buffer, 100 mM NaCl and 10% loading buffer, 20% polyacrylamide gel with a 10% loading gel, 1 h 40 min, 4 °C, 170 V, 6 mA, 2 W. Left lane: DNA ladder.